How to write gradual heating config files

From: Cristina Rodríguez (
Date: Mon Feb 14 2011 - 19:08:07 CST

Dear NAMD users!!!!

Along many tutorials and papers one could find some basic protocol for running a MD simulation, i.e.

1. Minimization
2. Heating
3. Equilibration
4. Production

The second step (Heating) is recommended to take the system in a gentle way from 0 K to the desired temperature running short simulations in steps of low increments.

On NAMD there are several ways to handle T control:

a) Changing velocities and/or

b) reassigning temperature (I came upon this thread in NAMD-L archive:

As an example, in case you use (a) the config file contains a loop to increment the temperature in step:

for {set TEMP 0} {$TEMP <=310} {incr TEMP 5} {
  langevinTemp $TEMP
  output md.$TEMP
run 2000 ; #2ps

On contrary, if you use (b) the config file contains something like that:

reassignFreq 5
reassignTemp 0
reassignIncr 1
reassignHold 310

Which method is best suited for this purpose? Which are the main differences between them?

Any comment would be really appreciated!!!!!



Cristina Rodríguez-Rodríguez, PhD
Department of Chemistry
University of British Columbia
Lab D419 - 2036 Main Mall
Vancouver, BC
Canada V6T 2A3

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